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Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

Creator: Tomar, V.
Creator: Dhillon, G.S.
Creator: Singh, D.
Creator: Singh, R.P.
Creator: Poland, J.A.
Creator: Joshi, A.K.
Creator: Tiwari, B.S.
Creator: Kumar, U.
Year: 2021
URI: https://hdl.handle.net/10883/21794
Language: English
Publisher: PeerJ Inc.
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
Type: Article
Place of Publication: USA
Volume: 9
DOI: 10.7717/peerj.11593
Keywords: Genotyping by Sequencing
Keywords: Analysis of Molecular Variance
Description: Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.
Agrovoc: WHEAT
Agrovoc: GENOTYPING
Agrovoc: SINGLE NUCLEOTIDE POLYMORPHISM
Agrovoc: GENETIC DIVERSITY
Agrovoc: POPULATION STRUCTURE
Agrovoc: ANALYSIS OF VARIANCE
Related Datasets: https://peerj.com/articles/11593/#supplemental-information
Elocator: 11593
ISSN: 2167-8359
Journal: PeerJ


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  • Wheat
    Wheat - breeding, phytopathology, physiology, quality, biotech

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